Starting phenix.real_space_refine on Fri Dec 8 14:02:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5y_15199/12_2023/8a5y_15199.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5y_15199/12_2023/8a5y_15199.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5y_15199/12_2023/8a5y_15199.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5y_15199/12_2023/8a5y_15199.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5y_15199/12_2023/8a5y_15199.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5y_15199/12_2023/8a5y_15199.pdb" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 3 6.06 5 S 301 5.16 5 C 37258 2.51 5 N 9537 2.21 5 O 10767 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 591": "OD1" <-> "OD2" Residue "J PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 284": "OE1" <-> "OE2" Residue "J ASP 582": "OD1" <-> "OD2" Residue "K PHE 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 632": "OD1" <-> "OD2" Residue "K ASP 705": "OD1" <-> "OD2" Residue "W ASP 21": "OD1" <-> "OD2" Residue "H GLU 172": "OE1" <-> "OE2" Residue "H TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 632": "OE1" <-> "OE2" Residue "E GLU 180": "OE1" <-> "OE2" Residue "E GLU 247": "OE1" <-> "OE2" Residue "T TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C GLU 469": "OE1" <-> "OE2" Residue "C GLU 526": "OE1" <-> "OE2" Residue "C PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 566": "OD1" <-> "OD2" Residue "C GLU 575": "OE1" <-> "OE2" Residue "C TYR 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 772": "OD1" <-> "OD2" Residue "C TYR 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 922": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1070": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1415": "OE1" <-> "OE2" Residue "O TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 320": "OD1" <-> "OD2" Residue "O PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 364": "OE1" <-> "OE2" Residue "O TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 437": "OE1" <-> "OE2" Residue "O TYR 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 536": "OE1" <-> "OE2" Residue "O GLU 590": "OE1" <-> "OE2" Residue "D GLU 254": "OE1" <-> "OE2" Residue "D PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 452": "OE1" <-> "OE2" Residue "P GLU 23": "OE1" <-> "OE2" Residue "P PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 254": "OE1" <-> "OE2" Residue "P ASP 257": "OD1" <-> "OD2" Residue "P PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 349": "OE1" <-> "OE2" Residue "P TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 459": "OD1" <-> "OD2" Residue "P TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 342": "OE1" <-> "OE2" Residue "Q GLU 391": "OE1" <-> "OE2" Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 57866 Number of models: 1 Model: "" Number of chains: 18 Chain: "F" Number of atoms: 3991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3991 Classifications: {'peptide': 502} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 14, 'TRANS': 487} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "J" Number of atoms: 4124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 4124 Classifications: {'peptide': 509} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 496} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "K" Number of atoms: 4102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 4102 Classifications: {'peptide': 505} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 492} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 284 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "W" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 284 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "H" Number of atoms: 4038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 4038 Classifications: {'peptide': 505} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 490} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1091 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "T" Number of atoms: 5362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5362 Classifications: {'peptide': 650} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 627} Chain breaks: 5 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 4, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "U" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 912 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain breaks: 1 Chain: "C" Number of atoms: 10832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1406, 10832 Classifications: {'peptide': 1406} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PCIS': 2, 'PTRANS': 57, 'TRANS': 1346} Chain breaks: 12 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 376 Unresolved non-hydrogen angles: 437 Unresolved non-hydrogen dihedrals: 329 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 4, 'GLU:plan': 13, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 204 Chain: "O" Number of atoms: 5285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5285 Classifications: {'peptide': 658} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 17, 'TRANS': 640} Chain breaks: 1 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 7, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 57 Chain: "D" Number of atoms: 4524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4524 Classifications: {'peptide': 560} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 7, 'TRANS': 552} Chain breaks: 2 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'HIS:plan': 1, 'ARG:plan': 5, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 75 Chain: "P" Number of atoms: 4520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 556, 4520 Classifications: {'peptide': 556} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 7, 'TRANS': 548} Chain breaks: 2 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 58 Chain: "I" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 906 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 107} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 784 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "Q" Number of atoms: 5086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 5086 Classifications: {'peptide': 623} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 602} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1738 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "U" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 23560 SG CYS U 52 148.796 81.544 156.273 1.00902.75 S ATOM 23579 SG CYS U 55 148.465 83.117 159.554 1.00868.86 S ATOM 23633 SG CYS U 62 150.496 79.919 159.170 1.00857.38 S ATOM 23681 SG CYS U 69 143.181 64.053 153.976 1.00975.71 S ATOM 23869 SG CYS U 91 143.377 66.901 151.484 1.001008.8 S ATOM 23890 SG CYS U 94 142.846 63.471 150.518 1.00997.18 S ATOM 23483 SG CYS U 41 149.495 75.070 153.130 1.00949.03 S ATOM 23501 SG CYS U 44 151.192 78.008 152.689 1.00957.51 S ATOM 23754 SG CYS U 77 147.842 78.142 153.881 1.00986.59 S Time building chain proxies: 22.17, per 1000 atoms: 0.38 Number of scatterers: 57866 At special positions: 0 Unit cell: (264.96, 212.52, 204.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 3 29.99 S 301 16.00 O 10767 8.00 N 9537 7.00 C 37258 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS J 482 " - pdb=" SG CYS J 506 " distance=2.05 Simple disulfide: pdb=" SG CYS K 482 " - pdb=" SG CYS K 506 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.62 Conformation dependent library (CDL) restraints added in 7.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN U 201 " pdb="ZN ZN U 201 " - pdb=" ND1 HIS U 76 " pdb="ZN ZN U 201 " - pdb=" SG CYS U 55 " pdb="ZN ZN U 201 " - pdb=" SG CYS U 52 " pdb="ZN ZN U 201 " - pdb=" SG CYS U 62 " pdb=" ZN U 202 " pdb="ZN ZN U 202 " - pdb=" SG CYS U 91 " pdb="ZN ZN U 202 " - pdb=" SG CYS U 94 " pdb="ZN ZN U 202 " - pdb=" SG CYS U 69 " pdb="ZN ZN U 202 " - pdb=" ND1 HIS U 71 " pdb=" ZN U 203 " pdb="ZN ZN U 203 " - pdb=" SG CYS U 44 " pdb="ZN ZN U 203 " - pdb=" SG CYS U 77 " pdb="ZN ZN U 203 " - pdb=" SG CYS U 41 " pdb="ZN ZN U 203 " - pdb=" ND1 HIS U 74 " Number of angles added : 9 14202 Ramachandran restraints generated. 7101 Oldfield, 0 Emsley, 7101 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13910 Finding SS restraints... Secondary structure from input PDB file: 352 helices and 29 sheets defined 68.6% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.15 Creating SS restraints... Processing helix chain 'F' and resid 24 through 40 Processing helix chain 'F' and resid 44 through 61 removed outlier: 4.349A pdb=" N PHE F 48 " --> pdb=" O SER F 44 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU F 49 " --> pdb=" O THR F 45 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE F 59 " --> pdb=" O ALA F 55 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP F 61 " --> pdb=" O CYS F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 81 Processing helix chain 'F' and resid 83 through 94 removed outlier: 3.768A pdb=" N ALA F 87 " --> pdb=" O SER F 83 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLN F 89 " --> pdb=" O HIS F 85 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE F 94 " --> pdb=" O ILE F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 113 Processing helix chain 'F' and resid 115 through 132 removed outlier: 3.734A pdb=" N ALA F 119 " --> pdb=" O GLY F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 168 removed outlier: 3.521A pdb=" N CYS F 158 " --> pdb=" O ALA F 154 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP F 168 " --> pdb=" O TYR F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 184 removed outlier: 4.163A pdb=" N GLY F 173 " --> pdb=" O HIS F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 197 removed outlier: 3.543A pdb=" N TYR F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N MET F 197 " --> pdb=" O ALA F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 209 Processing helix chain 'F' and resid 433 through 450 Processing helix chain 'F' and resid 451 through 462 removed outlier: 3.849A pdb=" N ALA F 455 " --> pdb=" O ASN F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 464 through 469 Processing helix chain 'F' and resid 471 through 485 Processing helix chain 'F' and resid 488 through 502 Processing helix chain 'F' and resid 509 through 520 Processing helix chain 'F' and resid 522 through 536 Processing helix chain 'F' and resid 539 through 554 removed outlier: 3.658A pdb=" N TRP F 543 " --> pdb=" O LYS F 539 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS F 554 " --> pdb=" O LEU F 550 " (cutoff:3.500A) Processing helix chain 'F' and resid 556 through 570 Processing helix chain 'F' and resid 573 through 587 removed outlier: 3.625A pdb=" N TYR F 577 " --> pdb=" O PHE F 573 " (cutoff:3.500A) Processing helix chain 'F' and resid 589 through 604 Processing helix chain 'F' and resid 607 through 622 Processing helix chain 'F' and resid 623 through 638 removed outlier: 3.662A pdb=" N ALA F 627 " --> pdb=" O GLN F 623 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE F 637 " --> pdb=" O LYS F 633 " (cutoff:3.500A) Processing helix chain 'F' and resid 641 through 656 Processing helix chain 'F' and resid 657 through 672 removed outlier: 3.699A pdb=" N GLN F 663 " --> pdb=" O GLU F 659 " (cutoff:3.500A) Processing helix chain 'F' and resid 675 through 689 Processing helix chain 'F' and resid 691 through 706 removed outlier: 4.007A pdb=" N GLN F 697 " --> pdb=" O ASN F 693 " (cutoff:3.500A) Processing helix chain 'F' and resid 709 through 724 removed outlier: 3.809A pdb=" N HIS F 713 " --> pdb=" O ASP F 709 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR F 714 " --> pdb=" O ALA F 710 " (cutoff:3.500A) Processing helix chain 'F' and resid 725 through 740 removed outlier: 3.642A pdb=" N LYS F 731 " --> pdb=" O LYS F 727 " (cutoff:3.500A) Processing helix chain 'F' and resid 743 through 755 Processing helix chain 'J' and resid 230 through 243 Processing helix chain 'J' and resid 245 through 260 Processing helix chain 'J' and resid 262 through 276 removed outlier: 3.641A pdb=" N ASN J 276 " --> pdb=" O VAL J 272 " (cutoff:3.500A) Processing helix chain 'J' and resid 278 through 289 removed outlier: 4.044A pdb=" N ASN J 289 " --> pdb=" O LEU J 285 " (cutoff:3.500A) Processing helix chain 'J' and resid 295 through 309 removed outlier: 3.715A pdb=" N ARG J 299 " --> pdb=" O ASN J 295 " (cutoff:3.500A) Processing helix chain 'J' and resid 311 through 320 Processing helix chain 'J' and resid 356 through 372 removed outlier: 3.612A pdb=" N SER J 360 " --> pdb=" O LYS J 356 " (cutoff:3.500A) Processing helix chain 'J' and resid 374 through 389 removed outlier: 3.604A pdb=" N ASP J 380 " --> pdb=" O ASN J 376 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP J 389 " --> pdb=" O ALA J 385 " (cutoff:3.500A) Processing helix chain 'J' and resid 393 through 403 Processing helix chain 'J' and resid 406 through 417 Processing helix chain 'J' and resid 422 through 424 No H-bonds generated for 'chain 'J' and resid 422 through 424' Processing helix chain 'J' and resid 425 through 436 removed outlier: 4.231A pdb=" N ASN J 436 " --> pdb=" O LEU J 432 " (cutoff:3.500A) Processing helix chain 'J' and resid 442 through 457 removed outlier: 3.744A pdb=" N ILE J 446 " --> pdb=" O ASN J 442 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR J 457 " --> pdb=" O LEU J 453 " (cutoff:3.500A) Processing helix chain 'J' and resid 462 through 476 Processing helix chain 'J' and resid 478 through 491 Processing helix chain 'J' and resid 499 through 511 Processing helix chain 'J' and resid 512 through 527 removed outlier: 3.592A pdb=" N THR J 526 " --> pdb=" O ARG J 522 " (cutoff:3.500A) Processing helix chain 'J' and resid 530 through 544 removed outlier: 4.076A pdb=" N TRP J 534 " --> pdb=" O SER J 530 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU J 544 " --> pdb=" O TYR J 540 " (cutoff:3.500A) Processing helix chain 'J' and resid 546 through 561 removed outlier: 4.244A pdb=" N LYS J 552 " --> pdb=" O SER J 548 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR J 553 " --> pdb=" O GLU J 549 " (cutoff:3.500A) Processing helix chain 'J' and resid 564 through 578 removed outlier: 3.647A pdb=" N TRP J 568 " --> pdb=" O PHE J 564 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU J 578 " --> pdb=" O THR J 574 " (cutoff:3.500A) Processing helix chain 'J' and resid 580 through 595 removed outlier: 3.911A pdb=" N ALA J 584 " --> pdb=" O GLU J 580 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU J 585 " --> pdb=" O GLN J 581 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR J 586 " --> pdb=" O ASP J 582 " (cutoff:3.500A) Processing helix chain 'J' and resid 598 through 612 removed outlier: 4.418A pdb=" N LYS J 602 " --> pdb=" O MET J 598 " (cutoff:3.500A) Processing helix chain 'J' and resid 615 through 629 Processing helix chain 'J' and resid 632 through 646 Processing helix chain 'J' and resid 650 through 663 Processing helix chain 'J' and resid 672 through 687 Processing helix chain 'J' and resid 689 through 704 removed outlier: 3.633A pdb=" N ALA J 693 " --> pdb=" O GLU J 689 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS J 695 " --> pdb=" O GLU J 691 " (cutoff:3.500A) Processing helix chain 'J' and resid 707 through 721 removed outlier: 3.699A pdb=" N HIS J 711 " --> pdb=" O ASN J 707 " (cutoff:3.500A) Processing helix chain 'J' and resid 723 through 738 removed outlier: 4.388A pdb=" N ASP J 729 " --> pdb=" O GLN J 725 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N HIS J 730 " --> pdb=" O LYS J 726 " (cutoff:3.500A) Processing helix chain 'J' and resid 741 through 758 Processing helix chain 'K' and resid 230 through 244 Processing helix chain 'K' and resid 245 through 261 Processing helix chain 'K' and resid 262 through 276 Processing helix chain 'K' and resid 278 through 289 removed outlier: 3.751A pdb=" N ALA K 282 " --> pdb=" O GLN K 278 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ASN K 289 " --> pdb=" O LEU K 285 " (cutoff:3.500A) Processing helix chain 'K' and resid 290 through 294 removed outlier: 3.988A pdb=" N GLY K 293 " --> pdb=" O ASN K 290 " (cutoff:3.500A) Processing helix chain 'K' and resid 296 through 309 removed outlier: 3.792A pdb=" N TYR K 300 " --> pdb=" O ILE K 296 " (cutoff:3.500A) Processing helix chain 'K' and resid 312 through 320 Processing helix chain 'K' and resid 356 through 372 removed outlier: 3.671A pdb=" N SER K 360 " --> pdb=" O LYS K 356 " (cutoff:3.500A) Processing helix chain 'K' and resid 374 through 389 Processing helix chain 'K' and resid 392 through 402 removed outlier: 3.871A pdb=" N PHE K 396 " --> pdb=" O ASN K 392 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU K 399 " --> pdb=" O ALA K 395 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS K 402 " --> pdb=" O MET K 398 " (cutoff:3.500A) Processing helix chain 'K' and resid 406 through 417 Processing helix chain 'K' and resid 419 through 423 Processing helix chain 'K' and resid 425 through 436 removed outlier: 4.367A pdb=" N ASN K 431 " --> pdb=" O GLU K 427 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN K 436 " --> pdb=" O LEU K 432 " (cutoff:3.500A) Processing helix chain 'K' and resid 442 through 455 removed outlier: 3.701A pdb=" N ILE K 446 " --> pdb=" O ASN K 442 " (cutoff:3.500A) Processing helix chain 'K' and resid 458 through 461 removed outlier: 4.387A pdb=" N ASP K 461 " --> pdb=" O LYS K 458 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 458 through 461' Processing helix chain 'K' and resid 462 through 476 Processing helix chain 'K' and resid 478 through 493 removed outlier: 4.121A pdb=" N ASN K 492 " --> pdb=" O THR K 488 " (cutoff:3.500A) Processing helix chain 'K' and resid 499 through 511 Processing helix chain 'K' and resid 512 through 527 removed outlier: 4.171A pdb=" N LEU K 516 " --> pdb=" O ASN K 512 " (cutoff:3.500A) Processing helix chain 'K' and resid 530 through 544 removed outlier: 4.132A pdb=" N TRP K 534 " --> pdb=" O SER K 530 " (cutoff:3.500A) Processing helix chain 'K' and resid 546 through 561 removed outlier: 3.794A pdb=" N LYS K 552 " --> pdb=" O SER K 548 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER K 557 " --> pdb=" O TYR K 553 " (cutoff:3.500A) Processing helix chain 'K' and resid 564 through 579 removed outlier: 4.011A pdb=" N TRP K 568 " --> pdb=" O PHE K 564 " (cutoff:3.500A) Processing helix chain 'K' and resid 581 through 595 removed outlier: 3.596A pdb=" N THR K 586 " --> pdb=" O ASP K 582 " (cutoff:3.500A) Processing helix chain 'K' and resid 598 through 612 removed outlier: 4.407A pdb=" N LYS K 602 " --> pdb=" O MET K 598 " (cutoff:3.500A) Processing helix chain 'K' and resid 614 through 627 removed outlier: 3.881A pdb=" N ALA K 618 " --> pdb=" O SER K 614 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER K 620 " --> pdb=" O ASN K 616 " (cutoff:3.500A) Processing helix chain 'K' and resid 632 through 646 removed outlier: 3.541A pdb=" N LEU K 636 " --> pdb=" O ASP K 632 " (cutoff:3.500A) Processing helix chain 'K' and resid 648 through 665 removed outlier: 3.831A pdb=" N ALA K 652 " --> pdb=" O GLU K 648 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ASP K 665 " --> pdb=" O GLU K 661 " (cutoff:3.500A) Processing helix chain 'K' and resid 672 through 688 Processing helix chain 'K' and resid 690 through 704 Processing helix chain 'K' and resid 707 through 721 Processing helix chain 'K' and resid 723 through 738 Processing helix chain 'K' and resid 741 through 758 removed outlier: 3.846A pdb=" N THR K 745 " --> pdb=" O ASN K 741 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA K 746 " --> pdb=" O SER K 742 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 29 removed outlier: 3.715A pdb=" N VAL G 16 " --> pdb=" O SER G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 35 removed outlier: 3.613A pdb=" N ASN G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'W' and resid 12 through 35 removed outlier: 3.918A pdb=" N VAL W 16 " --> pdb=" O SER W 12 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLN W 30 " --> pdb=" O GLN W 26 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN W 31 " --> pdb=" O LYS W 27 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU W 32 " --> pdb=" O LEU W 28 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN W 33 " --> pdb=" O LYS W 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 40 removed outlier: 3.524A pdb=" N GLN H 40 " --> pdb=" O GLN H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 57 Processing helix chain 'H' and resid 64 through 81 removed outlier: 3.763A pdb=" N SER H 68 " --> pdb=" O SER H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 94 removed outlier: 3.860A pdb=" N PHE H 94 " --> pdb=" O ILE H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 113 Processing helix chain 'H' and resid 115 through 131 removed outlier: 3.557A pdb=" N ALA H 119 " --> pdb=" O GLY H 115 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER H 125 " --> pdb=" O LEU H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 167 removed outlier: 3.678A pdb=" N ASN H 157 " --> pdb=" O LEU H 153 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N CYS H 158 " --> pdb=" O ALA H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 184 Processing helix chain 'H' and resid 188 through 197 removed outlier: 3.745A pdb=" N GLU H 192 " --> pdb=" O TRP H 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 209 Processing helix chain 'H' and resid 433 through 449 Processing helix chain 'H' and resid 451 through 463 removed outlier: 3.546A pdb=" N ILE H 463 " --> pdb=" O PHE H 459 " (cutoff:3.500A) Processing helix chain 'H' and resid 464 through 469 Processing helix chain 'H' and resid 471 through 485 Processing helix chain 'H' and resid 487 through 502 removed outlier: 3.506A pdb=" N SER H 491 " --> pdb=" O ASN H 487 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU H 492 " --> pdb=" O TYR H 488 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS H 493 " --> pdb=" O ASP H 489 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR H 494 " --> pdb=" O MET H 490 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG H 497 " --> pdb=" O LYS H 493 " (cutoff:3.500A) Processing helix chain 'H' and resid 509 through 520 Processing helix chain 'H' and resid 521 through 536 Processing helix chain 'H' and resid 539 through 554 removed outlier: 3.761A pdb=" N TRP H 543 " --> pdb=" O LYS H 539 " (cutoff:3.500A) Processing helix chain 'H' and resid 556 through 570 Processing helix chain 'H' and resid 573 through 587 removed outlier: 3.698A pdb=" N TYR H 577 " --> pdb=" O PHE H 573 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER H 585 " --> pdb=" O GLY H 581 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N SER H 586 " --> pdb=" O HIS H 582 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN H 587 " --> pdb=" O GLU H 583 " (cutoff:3.500A) Processing helix chain 'H' and resid 590 through 604 removed outlier: 3.507A pdb=" N CYS H 603 " --> pdb=" O LYS H 599 " (cutoff:3.500A) Processing helix chain 'H' and resid 608 through 621 removed outlier: 3.597A pdb=" N LEU H 621 " --> pdb=" O SER H 617 " (cutoff:3.500A) Processing helix chain 'H' and resid 623 through 638 removed outlier: 3.542A pdb=" N LYS H 633 " --> pdb=" O LEU H 629 " (cutoff:3.500A) Processing helix chain 'H' and resid 642 through 656 Processing helix chain 'H' and resid 657 through 672 Processing helix chain 'H' and resid 675 through 689 Processing helix chain 'H' and resid 691 through 706 removed outlier: 4.362A pdb=" N GLN H 697 " --> pdb=" O ASN H 693 " (cutoff:3.500A) Processing helix chain 'H' and resid 709 through 724 removed outlier: 3.642A pdb=" N HIS H 713 " --> pdb=" O ASP H 709 " (cutoff:3.500A) Processing helix chain 'H' and resid 725 through 740 Processing helix chain 'H' and resid 743 through 755 removed outlier: 3.678A pdb=" N ILE H 747 " --> pdb=" O GLY H 743 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 123 Processing helix chain 'E' and resid 169 through 178 Processing helix chain 'E' and resid 192 through 207 removed outlier: 3.643A pdb=" N LEU E 203 " --> pdb=" O GLU E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 216 Processing helix chain 'E' and resid 217 through 240 removed outlier: 3.520A pdb=" N LEU E 221 " --> pdb=" O GLN E 217 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N HIS E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLU E 223 " --> pdb=" O HIS E 219 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU E 224 " --> pdb=" O HIS E 220 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN E 229 " --> pdb=" O TYR E 225 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU E 230 " --> pdb=" O LEU E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 258 removed outlier: 3.548A pdb=" N CYS E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ARG E 254 " --> pdb=" O ARG E 250 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG E 255 " --> pdb=" O ASP E 251 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N HIS E 256 " --> pdb=" O LYS E 252 " (cutoff:3.500A) Processing helix chain 'T' and resid 10 through 27 Processing helix chain 'T' and resid 30 through 42 Processing helix chain 'T' and resid 56 through 67 removed outlier: 3.511A pdb=" N LYS T 60 " --> pdb=" O SER T 56 " (cutoff:3.500A) Processing helix chain 'T' and resid 93 through 121 Processing helix chain 'T' and resid 122 through 125 removed outlier: 3.567A pdb=" N ILE T 125 " --> pdb=" O PHE T 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 122 through 125' Processing helix chain 'T' and resid 127 through 145 removed outlier: 3.641A pdb=" N ILE T 131 " --> pdb=" O TYR T 127 " (cutoff:3.500A) Proline residue: T 141 - end of helix removed outlier: 4.331A pdb=" N TYR T 144 " --> pdb=" O PHE T 140 " (cutoff:3.500A) Processing helix chain 'T' and resid 153 through 170 Processing helix chain 'T' and resid 170 through 187 Processing helix chain 'T' and resid 189 through 204 Processing helix chain 'T' and resid 208 through 229 removed outlier: 3.833A pdb=" N LEU T 212 " --> pdb=" O SER T 208 " (cutoff:3.500A) Processing helix chain 'T' and resid 237 through 259 removed outlier: 3.596A pdb=" N GLU T 241 " --> pdb=" O PHE T 237 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N SER T 252 " --> pdb=" O ASN T 248 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N GLN T 253 " --> pdb=" O GLN T 249 " (cutoff:3.500A) Processing helix chain 'T' and resid 264 through 293 removed outlier: 5.342A pdb=" N PHE T 288 " --> pdb=" O THR T 284 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ASP T 289 " --> pdb=" O ASN T 285 " (cutoff:3.500A) Processing helix chain 'T' and resid 298 through 309 removed outlier: 3.631A pdb=" N ILE T 308 " --> pdb=" O GLU T 304 " (cutoff:3.500A) Processing helix chain 'T' and resid 311 through 330 Processing helix chain 'T' and resid 336 through 355 Processing helix chain 'T' and resid 358 through 375 Proline residue: T 370 - end of helix Processing helix chain 'T' and resid 377 through 387 Processing helix chain 'T' and resid 390 through 398 removed outlier: 4.224A pdb=" N LYS T 397 " --> pdb=" O GLU T 393 " (cutoff:3.500A) Processing helix chain 'T' and resid 403 through 416 Processing helix chain 'T' and resid 456 through 468 removed outlier: 3.573A pdb=" N TYR T 460 " --> pdb=" O HIS T 456 " (cutoff:3.500A) Processing helix chain 'T' and resid 490 through 497 removed outlier: 3.665A pdb=" N VAL T 494 " --> pdb=" O ASN T 490 " (cutoff:3.500A) Processing helix chain 'T' and resid 501 through 520 removed outlier: 4.535A pdb=" N PHE T 505 " --> pdb=" O SER T 501 " (cutoff:3.500A) Processing helix chain 'T' and resid 526 through 544 removed outlier: 3.706A pdb=" N THR T 530 " --> pdb=" O ASP T 526 " (cutoff:3.500A) Processing helix chain 'T' and resid 568 through 599 removed outlier: 4.490A pdb=" N SER T 576 " --> pdb=" O SER T 572 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ILE T 577 " --> pdb=" O ASN T 573 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ASP T 578 " --> pdb=" O LEU T 574 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL T 579 " --> pdb=" O ASN T 575 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG T 592 " --> pdb=" O GLU T 588 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY T 599 " --> pdb=" O HIS T 595 " (cutoff:3.500A) Processing helix chain 'T' and resid 631 through 649 Processing helix chain 'T' and resid 681 through 689 removed outlier: 3.620A pdb=" N GLN T 689 " --> pdb=" O SER T 685 " (cutoff:3.500A) Processing helix chain 'T' and resid 702 through 710 Processing helix chain 'T' and resid 712 through 726 Processing helix chain 'U' and resid 58 through 62 removed outlier: 4.099A pdb=" N GLN U 61 " --> pdb=" O PRO U 58 " (cutoff:3.500A) Processing helix chain 'U' and resid 75 through 84 Processing helix chain 'U' and resid 110 through 128 Processing helix chain 'C' and resid 391 through 397 removed outlier: 3.589A pdb=" N LYS C 397 " --> pdb=" O SER C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 435 Processing helix chain 'C' and resid 435 through 442 removed outlier: 3.524A pdb=" N LYS C 439 " --> pdb=" O SER C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 460 No H-bonds generated for 'chain 'C' and resid 458 through 460' Processing helix chain 'C' and resid 507 through 513 removed outlier: 3.641A pdb=" N THR C 510 " --> pdb=" O GLU C 507 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS C 511 " --> pdb=" O GLU C 508 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N GLN C 512 " --> pdb=" O LEU C 509 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASN C 513 " --> pdb=" O THR C 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 507 through 513' Processing helix chain 'C' and resid 514 through 520 Processing helix chain 'C' and resid 529 through 541 removed outlier: 3.835A pdb=" N CYS C 533 " --> pdb=" O PHE C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 564 Processing helix chain 'C' and resid 571 through 588 removed outlier: 4.011A pdb=" N GLU C 575 " --> pdb=" O GLY C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 601 Processing helix chain 'C' and resid 601 through 606 removed outlier: 3.666A pdb=" N TYR C 605 " --> pdb=" O TYR C 601 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU C 606 " --> pdb=" O LYS C 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 601 through 606' Processing helix chain 'C' and resid 607 through 616 Processing helix chain 'C' and resid 616 through 640 removed outlier: 3.567A pdb=" N THR C 620 " --> pdb=" O ASP C 616 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU C 624 " --> pdb=" O THR C 620 " (cutoff:3.500A) Proline residue: C 625 - end of helix removed outlier: 3.626A pdb=" N LEU C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 643 No H-bonds generated for 'chain 'C' and resid 641 through 643' Processing helix chain 'C' and resid 644 through 663 removed outlier: 3.599A pdb=" N HIS C 648 " --> pdb=" O CYS C 644 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE C 654 " --> pdb=" O LEU C 650 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 671 removed outlier: 3.610A pdb=" N GLN C 669 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 710 Processing helix chain 'C' and resid 731 through 737 removed outlier: 3.770A pdb=" N GLU C 735 " --> pdb=" O ASP C 731 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG C 737 " --> pdb=" O GLN C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 753 removed outlier: 3.832A pdb=" N HIS C 753 " --> pdb=" O TYR C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 769 Processing helix chain 'C' and resid 772 through 778 Processing helix chain 'C' and resid 783 through 798 removed outlier: 4.327A pdb=" N LEU C 787 " --> pdb=" O ILE C 783 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN C 788 " --> pdb=" O LEU C 784 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN C 789 " --> pdb=" O VAL C 785 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASP C 796 " --> pdb=" O LYS C 792 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS C 797 " --> pdb=" O ILE C 793 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU C 798 " --> pdb=" O LEU C 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 808 removed outlier: 4.044A pdb=" N LEU C 807 " --> pdb=" O ASN C 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 810 through 826 removed outlier: 3.639A pdb=" N GLN C 814 " --> pdb=" O ARG C 810 " (cutoff:3.500A) Processing helix chain 'C' and resid 859 through 872 removed outlier: 3.722A pdb=" N SER C 872 " --> pdb=" O VAL C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 906 Processing helix chain 'C' and resid 910 through 920 Processing helix chain 'C' and resid 935 through 965 removed outlier: 4.888A pdb=" N GLY C 958 " --> pdb=" O THR C 954 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N VAL C 959 " --> pdb=" O CYS C 955 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLY C 960 " --> pdb=" O THR C 956 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA C 963 " --> pdb=" O VAL C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1021 removed outlier: 4.065A pdb=" N VAL C1007 " --> pdb=" O ALA C1003 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLU C1008 " --> pdb=" O HIS C1004 " (cutoff:3.500A) Processing helix chain 'C' and resid 1030 through 1037 removed outlier: 3.834A pdb=" N ILE C1034 " --> pdb=" O THR C1030 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA C1035 " --> pdb=" O GLY C1031 " (cutoff:3.500A) Processing helix chain 'C' and resid 1043 through 1057 removed outlier: 3.504A pdb=" N GLY C1057 " --> pdb=" O LEU C1053 " (cutoff:3.500A) Processing helix chain 'C' and resid 1063 through 1072 removed outlier: 3.711A pdb=" N ILE C1067 " --> pdb=" O GLU C1063 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N TYR C1068 " --> pdb=" O GLU C1064 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASN C1069 " --> pdb=" O TRP C1065 " (cutoff:3.500A) Processing helix chain 'C' and resid 1075 through 1091 removed outlier: 3.516A pdb=" N SER C1079 " --> pdb=" O ASN C1075 " (cutoff:3.500A) Processing helix chain 'C' and resid 1095 through 1106 removed outlier: 4.708A pdb=" N VAL C1101 " --> pdb=" O LYS C1097 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE C1102 " --> pdb=" O LEU C1098 " (cutoff:3.500A) Processing helix chain 'C' and resid 1120 through 1135 Processing helix chain 'C' and resid 1140 through 1153 removed outlier: 4.017A pdb=" N SER C1146 " --> pdb=" O ARG C1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 1164 through 1179 Processing helix chain 'C' and resid 1214 through 1230 Processing helix chain 'C' and resid 1242 through 1255 removed outlier: 4.552A pdb=" N GLY C1246 " --> pdb=" O ASN C1242 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE C1255 " --> pdb=" O ILE C1251 " (cutoff:3.500A) Processing helix chain 'C' and resid 1260 through 1268 Processing helix chain 'C' and resid 1270 through 1277 removed outlier: 3.668A pdb=" N LYS C1276 " --> pdb=" O LYS C1272 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1297 removed outlier: 4.151A pdb=" N MET C1287 " --> pdb=" O PRO C1283 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR C1288 " --> pdb=" O GLU C1284 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU C1297 " --> pdb=" O SER C1293 " (cutoff:3.500A) Processing helix chain 'C' and resid 1304 through 1309 removed outlier: 3.636A pdb=" N ILE C1308 " --> pdb=" O ASP C1304 " (cutoff:3.500A) Processing helix chain 'C' and resid 1322 through 1324 No H-bonds generated for 'chain 'C' and resid 1322 through 1324' Processing helix chain 'C' and resid 1325 through 1343 removed outlier: 3.759A pdb=" N TYR C1329 " --> pdb=" O LEU C1325 " (cutoff:3.500A) Processing helix chain 'C' and resid 1349 through 1363 Processing helix chain 'C' and resid 1373 through 1398 Processing helix chain 'C' and resid 1403 through 1415 removed outlier: 3.720A pdb=" N LEU C1407 " --> pdb=" O ASP C1403 " (cutoff:3.500A) Processing helix chain 'C' and resid 1476 through 1505 removed outlier: 3.581A pdb=" N ASP C1486 " --> pdb=" O GLU C1482 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER C1496 " --> pdb=" O GLY C1492 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR C1497 " --> pdb=" O LYS C1493 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE C1505 " --> pdb=" O LEU C1501 " (cutoff:3.500A) Processing helix chain 'C' and resid 1506 through 1510 Processing helix chain 'C' and resid 1517 through 1528 removed outlier: 3.641A pdb=" N ILE C1521 " --> pdb=" O THR C1517 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA C1522 " --> pdb=" O LEU C1518 " (cutoff:3.500A) Processing helix chain 'C' and resid 1538 through 1547 removed outlier: 4.182A pdb=" N HIS C1543 " --> pdb=" O GLU C1540 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N TRP C1545 " --> pdb=" O LYS C1542 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N SER C1546 " --> pdb=" O HIS C1543 " (cutoff:3.500A) Processing helix chain 'C' and resid 1595 through 1599 Processing helix chain 'C' and resid 1621 through 1626 Processing helix chain 'C' and resid 1653 through 1670 Processing helix chain 'C' and resid 1681 through 1690 Processing helix chain 'C' and resid 1693 through 1704 Processing helix chain 'C' and resid 1712 through 1724 Processing helix chain 'C' and resid 1730 through 1744 removed outlier: 3.509A pdb=" N LEU C1738 " --> pdb=" O CYS C1734 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 30 removed outlier: 3.534A pdb=" N CYS O 19 " --> pdb=" O PRO O 15 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE O 20 " --> pdb=" O TYR O 16 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN O 30 " --> pdb=" O ALA O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 49 removed outlier: 3.502A pdb=" N PHE O 41 " --> pdb=" O PRO O 37 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER O 46 " --> pdb=" O LEU O 42 " (cutoff:3.500A) Proline residue: O 47 - end of helix Processing helix chain 'O' and resid 77 through 87 removed outlier: 3.622A pdb=" N ILE O 84 " --> pdb=" O ASN O 80 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU O 85 " --> pdb=" O ILE O 81 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP O 87 " --> pdb=" O ARG O 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 105 removed outlier: 3.612A pdb=" N ILE O 94 " --> pdb=" O ASP O 90 " (cutoff:3.500A) Processing helix chain 'O' and resid 107 through 121 Processing helix chain 'O' and resid 126 through 130 Processing helix chain 'O' and resid 145 through 157 removed outlier: 3.560A pdb=" N PHE O 150 " --> pdb=" O PHE O 146 " (cutoff:3.500A) Processing helix chain 'O' and resid 162 through 182 removed outlier: 3.773A pdb=" N PHE O 180 " --> pdb=" O PHE O 176 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS O 182 " --> pdb=" O THR O 178 " (cutoff:3.500A) Processing helix chain 'O' and resid 183 through 189 removed outlier: 3.583A pdb=" N LEU O 187 " --> pdb=" O THR O 183 " (cutoff:3.500A) Processing helix chain 'O' and resid 193 through 204 removed outlier: 3.784A pdb=" N LEU O 202 " --> pdb=" O VAL O 198 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA O 204 " --> pdb=" O ASN O 200 " (cutoff:3.500A) Processing helix chain 'O' and resid 211 through 224 removed outlier: 4.152A pdb=" N MET O 215 " --> pdb=" O GLU O 211 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE O 218 " --> pdb=" O GLN O 214 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN O 220 " --> pdb=" O VAL O 216 " (cutoff:3.500A) Processing helix chain 'O' and resid 243 through 260 Processing helix chain 'O' and resid 279 through 288 Processing helix chain 'O' and resid 293 through 298 Processing helix chain 'O' and resid 299 through 312 removed outlier: 4.211A pdb=" N ILE O 303 " --> pdb=" O PRO O 299 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS O 305 " --> pdb=" O ILE O 301 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU O 308 " --> pdb=" O LEU O 304 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU O 312 " --> pdb=" O GLU O 308 " (cutoff:3.500A) Processing helix chain 'O' and resid 314 through 333 removed outlier: 3.607A pdb=" N ALA O 318 " --> pdb=" O SER O 314 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER O 330 " --> pdb=" O PHE O 326 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR O 331 " --> pdb=" O ASP O 327 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY O 332 " --> pdb=" O TYR O 328 " (cutoff:3.500A) Processing helix chain 'O' and resid 337 through 352 removed outlier: 3.551A pdb=" N LEU O 342 " --> pdb=" O PHE O 338 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU O 343 " --> pdb=" O HIS O 339 " (cutoff:3.500A) Processing helix chain 'O' and resid 355 through 373 removed outlier: 3.542A pdb=" N ASN O 360 " --> pdb=" O ASP O 356 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU O 364 " --> pdb=" O ASN O 360 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA O 365 " --> pdb=" O SER O 361 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR O 366 " --> pdb=" O PHE O 362 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG O 367 " --> pdb=" O GLU O 363 " (cutoff:3.500A) Processing helix chain 'O' and resid 375 through 392 removed outlier: 3.876A pdb=" N ASN O 379 " --> pdb=" O MET O 375 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU O 380 " --> pdb=" O GLU O 376 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE O 386 " --> pdb=" O MET O 382 " (cutoff:3.500A) Processing helix chain 'O' and resid 393 through 396 Processing helix chain 'O' and resid 402 through 412 removed outlier: 3.578A pdb=" N ILE O 406 " --> pdb=" O THR O 402 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASN O 412 " --> pdb=" O LYS O 408 " (cutoff:3.500A) Processing helix chain 'O' and resid 420 through 436 removed outlier: 3.809A pdb=" N LYS O 427 " --> pdb=" O SER O 423 " (cutoff:3.500A) Processing helix chain 'O' and resid 439 through 457 removed outlier: 3.879A pdb=" N ASN O 457 " --> pdb=" O ILE O 453 " (cutoff:3.500A) Processing helix chain 'O' and resid 462 through 481 Processing helix chain 'O' and resid 482 through 491 removed outlier: 3.600A pdb=" N VAL O 488 " --> pdb=" O SER O 484 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR O 489 " --> pdb=" O ILE O 485 " (cutoff:3.500A) Processing helix chain 'O' and resid 505 through 522 Processing helix chain 'O' and resid 524 through 536 removed outlier: 3.506A pdb=" N LYS O 534 " --> pdb=" O GLN O 530 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU O 536 " --> pdb=" O LEU O 532 " (cutoff:3.500A) Processing helix chain 'O' and resid 541 through 560 removed outlier: 3.590A pdb=" N ASN O 547 " --> pdb=" O ASP O 543 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL O 553 " --> pdb=" O LYS O 549 " (cutoff:3.500A) Processing helix chain 'O' and resid 562 through 579 removed outlier: 3.678A pdb=" N ASN O 570 " --> pdb=" O MET O 566 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN O 571 " --> pdb=" O ARG O 567 " (cutoff:3.500A) Processing helix chain 'O' and resid 582 through 600 removed outlier: 4.129A pdb=" N GLU O 592 " --> pdb=" O LYS O 588 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER O 593 " --> pdb=" O PHE O 589 " (cutoff:3.500A) Processing helix chain 'O' and resid 603 through 605 No H-bonds generated for 'chain 'O' and resid 603 through 605' Processing helix chain 'O' and resid 606 through 621 removed outlier: 3.534A pdb=" N LEU O 613 " --> pdb=" O LYS O 609 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE O 620 " --> pdb=" O GLU O 616 " (cutoff:3.500A) Processing helix chain 'O' and resid 622 through 639 removed outlier: 3.558A pdb=" N GLN O 639 " --> pdb=" O GLU O 635 " (cutoff:3.500A) Processing helix chain 'O' and resid 642 through 658 removed outlier: 3.817A pdb=" N ALA O 646 " --> pdb=" O LYS O 642 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N SER O 655 " --> pdb=" O SER O 651 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N THR O 656 " --> pdb=" O CYS O 652 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU O 658 " --> pdb=" O LEU O 654 " (cutoff:3.500A) Processing helix chain 'O' and resid 663 through 675 removed outlier: 3.502A pdb=" N GLU O 672 " --> pdb=" O ASP O 668 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER O 673 " --> pdb=" O GLU O 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 27 removed outlier: 3.582A pdb=" N ARG D 14 " --> pdb=" O ILE D 10 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE D 15 " --> pdb=" O HIS D 11 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 42 removed outlier: 3.880A pdb=" N SER D 33 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TRP D 35 " --> pdb=" O GLY D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 98 removed outlier: 4.129A pdb=" N LEU D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU D 90 " --> pdb=" O TYR D 86 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP D 97 " --> pdb=" O SER D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 108 Processing helix chain 'D' and resid 113 through 136 removed outlier: 3.795A pdb=" N LEU D 119 " --> pdb=" O TYR D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 201 removed outlier: 3.852A pdb=" N ILE D 190 " --> pdb=" O ASN D 186 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU D 193 " --> pdb=" O SER D 189 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE D 194 " --> pdb=" O ILE D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 227 removed outlier: 3.549A pdb=" N LEU D 220 " --> pdb=" O LEU D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 245 Processing helix chain 'D' and resid 248 through 259 removed outlier: 3.888A pdb=" N LEU D 259 " --> pdb=" O LEU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 274 Processing helix chain 'D' and resid 294 through 307 removed outlier: 3.574A pdb=" N PHE D 304 " --> pdb=" O LYS D 300 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU D 305 " --> pdb=" O LEU D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 325 Processing helix chain 'D' and resid 328 through 342 removed outlier: 3.599A pdb=" N LYS D 332 " --> pdb=" O PHE D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 359 removed outlier: 3.513A pdb=" N ALA D 348 " --> pdb=" O ASP D 344 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER D 350 " --> pdb=" O VAL D 346 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP D 354 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE D 355 " --> pdb=" O ARG D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 377 removed outlier: 3.885A pdb=" N TYR D 369 " --> pdb=" O ASP D 365 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL D 375 " --> pdb=" O ASN D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 393 removed outlier: 3.836A pdb=" N ILE D 392 " --> pdb=" O PHE D 388 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASP D 393 " --> pdb=" O VAL D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 410 removed outlier: 3.815A pdb=" N ILE D 403 " --> pdb=" O THR D 399 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA D 404 " --> pdb=" O CYS D 400 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG D 410 " --> pdb=" O TYR D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 427 removed outlier: 4.255A pdb=" N MET D 418 " --> pdb=" O GLU D 414 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR D 419 " --> pdb=" O LYS D 415 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE D 420 " --> pdb=" O SER D 416 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG D 421 " --> pdb=" O ILE D 417 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU D 426 " --> pdb=" O ARG D 422 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASP D 427 " --> pdb=" O ALA D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 443 removed outlier: 4.260A pdb=" N THR D 435 " --> pdb=" O THR D 431 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU D 436 " --> pdb=" O ASN D 432 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE D 441 " --> pdb=" O MET D 437 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL D 442 " --> pdb=" O GLY D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 461 removed outlier: 3.522A pdb=" N ALA D 450 " --> pdb=" O ASN D 446 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU D 452 " --> pdb=" O HIS D 448 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA D 457 " --> pdb=" O CYS D 453 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL D 458 " --> pdb=" O TYR D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 478 removed outlier: 3.537A pdb=" N ALA D 474 " --> pdb=" O GLY D 470 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR D 475 " --> pdb=" O LEU D 471 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU D 478 " --> pdb=" O ALA D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 483 No H-bonds generated for 'chain 'D' and resid 481 through 483' Processing helix chain 'D' and resid 484 through 495 removed outlier: 3.661A pdb=" N THR D 493 " --> pdb=" O GLN D 489 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU D 494 " --> pdb=" O LYS D 490 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS D 495 " --> pdb=" O ALA D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 512 removed outlier: 3.689A pdb=" N TRP D 502 " --> pdb=" O ASP D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 529 removed outlier: 4.165A pdb=" N LYS D 520 " --> pdb=" O VAL D 516 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS D 527 " --> pdb=" O LYS D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 534 Processing helix chain 'D' and resid 535 through 549 removed outlier: 3.631A pdb=" N TYR D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 569 removed outlier: 3.728A pdb=" N CYS D 555 " --> pdb=" O ASP D 551 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS D 556 " --> pdb=" O LEU D 552 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LYS D 557 " --> pdb=" O GLN D 553 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N PHE D 558 " --> pdb=" O GLU D 554 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU D 566 " --> pdb=" O CYS D 562 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU D 567 " --> pdb=" O VAL D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 591 removed outlier: 3.504A pdb=" N LYS D 579 " --> pdb=" O ASP D 575 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA D 580 " --> pdb=" O GLU D 576 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS D 590 " --> pdb=" O ILE D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 604 removed outlier: 3.503A pdb=" N ALA D 597 " --> pdb=" O ASN D 593 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP D 599 " --> pdb=" O GLN D 595 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N TYR D 600 " --> pdb=" O LEU D 596 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA D 601 " --> pdb=" O ALA D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 626 removed outlier: 3.613A pdb=" N GLU D 613 " --> pdb=" O SER D 609 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS D 625 " --> pdb=" O GLU D 621 " (cutoff:3.500A) Processing helix chain 'P' and resid 7 through 27 removed outlier: 3.808A pdb=" N HIS P 11 " --> pdb=" O ASP P 7 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU P 24 " --> pdb=" O ALA P 20 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER P 25 " --> pdb=" O ALA P 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 43 removed outlier: 3.589A pdb=" N TRP P 35 " --> pdb=" O GLY P 31 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA P 41 " --> pdb=" O ALA P 37 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 98 removed outlier: 3.854A pdb=" N ASP P 87 " --> pdb=" O GLU P 83 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N LEU P 88 " --> pdb=" O THR P 84 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR P 89 " --> pdb=" O GLU P 85 " (cutoff:3.500A) Processing helix chain 'P' and resid 100 through 108 removed outlier: 3.877A pdb=" N CYS P 104 " --> pdb=" O GLU P 100 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL P 105 " --> pdb=" O PHE P 101 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE P 106 " --> pdb=" O ASP P 102 " (cutoff:3.500A) Processing helix chain 'P' and resid 115 through 130 removed outlier: 4.009A pdb=" N LEU P 119 " --> pdb=" O TYR P 115 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS P 120 " --> pdb=" O LEU P 116 " (cutoff:3.500A) Processing helix chain 'P' and resid 134 through 143 removed outlier: 3.840A pdb=" N LEU P 140 " --> pdb=" O MET P 136 " (cutoff:3.500A) Processing helix chain 'P' and resid 184 through 201 removed outlier: 3.884A pdb=" N SER P 188 " --> pdb=" O GLN P 184 " (cutoff:3.500A) Processing helix chain 'P' and resid 211 through 228 removed outlier: 3.674A pdb=" N ALA P 215 " --> pdb=" O ASP P 211 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU P 216 " --> pdb=" O LEU P 212 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU P 228 " --> pdb=" O ILE P 224 " (cutoff:3.500A) Processing helix chain 'P' and resid 230 through 245 removed outlier: 3.934A pdb=" N SER P 236 " --> pdb=" O SER P 232 " (cutoff:3.500A) Processing helix chain 'P' and resid 248 through 257 removed outlier: 3.718A pdb=" N TRP P 252 " --> pdb=" O ASN P 248 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU P 254 " --> pdb=" O SER P 250 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP P 257 " --> pdb=" O LEU P 253 " (cutoff:3.500A) Processing helix chain 'P' and resid 262 through 274 removed outlier: 4.067A pdb=" N LEU P 266 " --> pdb=" O VAL P 262 " (cutoff:3.500A) Processing helix chain 'P' and resid 294 through 307 removed outlier: 3.674A pdb=" N PHE P 298 " --> pdb=" O ILE P 294 " (cutoff:3.500A) Processing helix chain 'P' and resid 313 through 324 removed outlier: 3.519A pdb=" N PHE P 320 " --> pdb=" O GLU P 316 " (cutoff:3.500A) Processing helix chain 'P' and resid 328 through 342 removed outlier: 3.757A pdb=" N SER P 339 " --> pdb=" O ASN P 335 " (cutoff:3.500A) Processing helix chain 'P' and resid 344 through 359 removed outlier: 3.853A pdb=" N SER P 350 " --> pdb=" O VAL P 346 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE P 355 " --> pdb=" O ARG P 351 " (cutoff:3.500A) Processing helix chain 'P' and resid 365 through 377 removed outlier: 4.073A pdb=" N TYR P 369 " --> pdb=" O ASP P 365 " (cutoff:3.500A) Processing helix chain 'P' and resid 378 through 393 removed outlier: 3.502A pdb=" N TYR P 384 " --> pdb=" O SER P 380 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE P 392 " --> pdb=" O PHE P 388 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP P 393 " --> pdb=" O VAL P 389 " (cutoff:3.500A) Processing helix chain 'P' and resid 396 through 410 removed outlier: 3.535A pdb=" N ALA P 409 " --> pdb=" O ASN P 405 " (cutoff:3.500A) Processing helix chain 'P' and resid 412 through 428 removed outlier: 3.829A pdb=" N ILE P 417 " --> pdb=" O HIS P 413 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N MET P 418 " --> pdb=" O GLU P 414 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR P 419 " --> pdb=" O LYS P 415 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU P 426 " --> pdb=" O ARG P 422 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP P 427 " --> pdb=" O ALA P 423 " (cutoff:3.500A) Processing helix chain 'P' and resid 432 through 445 removed outlier: 3.908A pdb=" N LEU P 436 " --> pdb=" O ASN P 432 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU P 440 " --> pdb=" O LEU P 436 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE P 441 " --> pdb=" O MET P 437 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU P 444 " --> pdb=" O GLU P 440 " (cutoff:3.500A) Processing helix chain 'P' and resid 448 through 461 removed outlier: 3.731A pdb=" N ALA P 457 " --> pdb=" O CYS P 453 " (cutoff:3.500A) Processing helix chain 'P' and resid 464 through 478 removed outlier: 3.569A pdb=" N TRP P 468 " --> pdb=" O ASP P 464 " (cutoff:3.500A) Processing helix chain 'P' and resid 481 through 495 removed outlier: 3.725A pdb=" N LEU P 485 " --> pdb=" O HIS P 481 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TYR P 486 " --> pdb=" O LEU P 482 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR P 487 " --> pdb=" O TYR P 483 " (cutoff:3.500A) Processing helix chain 'P' and resid 498 through 510 removed outlier: 4.139A pdb=" N TRP P 502 " --> pdb=" O ASP P 498 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN P 503 " --> pdb=" O ARG P 499 " (cutoff:3.500A) Processing helix chain 'P' and resid 511 through 513 No H-bonds generated for 'chain 'P' and resid 511 through 513' Processing helix chain 'P' and resid 514 through 529 removed outlier: 3.754A pdb=" N ALA P 518 " --> pdb=" O ASN P 514 " (cutoff:3.500A) Processing helix chain 'P' and resid 534 through 548 removed outlier: 4.346A pdb=" N ILE P 538 " --> pdb=" O GLN P 534 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR P 540 " --> pdb=" O THR P 536 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG P 541 " --> pdb=" O SER P 537 " (cutoff:3.500A) Processing helix chain 'P' and resid 551 through 569 removed outlier: 3.727A pdb=" N GLU P 567 " --> pdb=" O VAL P 563 " (cutoff:3.500A) Processing helix chain 'P' and resid 574 through 591 Processing helix chain 'P' and resid 593 through 602 removed outlier: 3.532A pdb=" N TYR P 600 " --> pdb=" O LEU P 596 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET P 602 " --> pdb=" O TYR P 598 " (cutoff:3.500A) Processing helix chain 'P' and resid 608 through 626 Processing helix chain 'I' and resid 18 through 24 removed outlier: 3.657A pdb=" N ILE I 22 " --> pdb=" O PRO I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 30 removed outlier: 3.595A pdb=" N ASP I 30 " --> pdb=" O TRP I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 45 removed outlier: 4.126A pdb=" N THR I 42 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N MET I 43 " --> pdb=" O ALA I 39 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA I 44 " --> pdb=" O ASN I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 90 Processing helix chain 'I' and resid 93 through 100 Processing helix chain 'I' and resid 147 through 160 removed outlier: 4.354A pdb=" N THR I 151 " --> pdb=" O ASP I 147 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN I 152 " --> pdb=" O ARG I 148 " (cutoff:3.500A) Processing helix chain 'N' and resid 8 through 20 removed outlier: 3.618A pdb=" N SER N 20 " --> pdb=" O LYS N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 87 No H-bonds generated for 'chain 'N' and resid 85 through 87' Processing helix chain 'N' and resid 95 through 113 Proline residue: N 109 - end of helix removed outlier: 4.062A pdb=" N ARG N 112 " --> pdb=" O LEU N 108 " (cutoff:3.500A) Processing helix chain 'N' and resid 114 through 116 No H-bonds generated for 'chain 'N' and resid 114 through 116' Processing helix chain 'N' and resid 128 through 140 removed outlier: 3.516A pdb=" N GLU N 132 " --> pdb=" O MET N 128 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET N 133 " --> pdb=" O TYR N 129 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG N 139 " --> pdb=" O ARG N 135 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 47 No H-bonds generated for 'chain 'Q' and resid 45 through 47' Processing helix chain 'Q' and resid 220 through 226 Processing helix chain 'Q' and resid 226 through 257 removed outlier: 3.517A pdb=" N LYS Q 240 " --> pdb=" O ILE Q 236 " (cutoff:3.500A) Processing helix chain 'Q' and resid 257 through 270 removed outlier: 3.787A pdb=" N TYR Q 261 " --> pdb=" O LEU Q 257 " (cutoff:3.500A) Processing helix chain 'Q' and resid 274 through 288 removed outlier: 3.797A pdb=" N SER Q 280 " --> pdb=" O GLY Q 276 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU Q 281 " --> pdb=" O LYS Q 277 " (cutoff:3.500A) Processing helix chain 'Q' and resid 292 through 301 Processing helix chain 'Q' and resid 303 through 329 removed outlier: 3.510A pdb=" N ARG Q 310 " --> pdb=" O LYS Q 306 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR Q 322 " --> pdb=" O ALA Q 318 " (cutoff:3.500A) Processing helix chain 'Q' and resid 329 through 355 removed outlier: 3.574A pdb=" N LEU Q 348 " --> pdb=" O LEU Q 344 " (cutoff:3.500A) Processing helix chain 'Q' and resid 363 through 411 removed outlier: 3.646A pdb=" N TRP Q 400 " --> pdb=" O LYS Q 396 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP Q 403 " --> pdb=" O ILE Q 399 " (cutoff:3.500A) Processing helix chain 'Q' and resid 418 through 422 removed outlier: 3.534A pdb=" N ASP Q 422 " --> pdb=" O PHE Q 419 " (cutoff:3.500A) Processing helix chain 'Q' and resid 424 through 437 removed outlier: 3.551A pdb=" N ASP Q 428 " --> pdb=" O TYR Q 424 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE Q 433 " --> pdb=" O LEU Q 429 " (cutoff:3.500A) Processing helix chain 'Q' and resid 438 through 443 removed outlier: 3.692A pdb=" N GLU Q 443 " --> pdb=" O LYS Q 439 " (cutoff:3.500A) Processing helix chain 'Q' and resid 444 through 447 removed outlier: 4.288A pdb=" N ILE Q 447 " --> pdb=" O PRO Q 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 444 through 447' Processing helix chain 'Q' and resid 449 through 471 Processing helix chain 'Q' and resid 471 through 479 Processing helix chain 'Q' and resid 488 through 493 removed outlier: 4.507A pdb=" N LYS Q 492 " --> pdb=" O VAL Q 488 " (cutoff:3.500A) Processing helix chain 'Q' and resid 558 through 562 removed outlier: 3.660A pdb=" N LYS Q 562 " --> pdb=" O ALA Q 559 " (cutoff:3.500A) Processing helix chain 'Q' and resid 565 through 569 Processing helix chain 'Q' and resid 576 through 586 removed outlier: 3.722A pdb=" N LEU Q 580 " --> pdb=" O VAL Q 576 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY Q 584 " --> pdb=" O LEU Q 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 14 Processing helix chain 'A' and resid 40 through 47 Processing helix chain 'A' and resid 61 through 79 removed outlier: 3.790A pdb=" N ALA A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 Processing sheet with id=AA1, first strand: chain 'T' and resid 607 through 610 removed outlier: 5.837A pdb=" N LYS T 607 " --> pdb=" O PHE U 12 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N TRP U 14 " --> pdb=" O LYS T 607 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE T 609 " --> pdb=" O TRP U 14 " (cutoff:3.500A) removed outlier: 8.941A pdb=" N TRP U 16 " --> pdb=" O ILE T 609 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLU T 664 " --> pdb=" O ASN U 6 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N VAL U 8 " --> pdb=" O LYS T 662 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LYS T 662 " --> pdb=" O VAL U 8 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N SER U 10 " --> pdb=" O LYS T 660 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N LYS T 660 " --> pdb=" O SER U 10 " (cutoff:3.500A) removed outlier: 9.776A pdb=" N PHE U 12 " --> pdb=" O LYS T 658 " (cutoff:3.500A) removed outlier: 9.229A pdb=" N LYS T 658 " --> pdb=" O PHE U 12 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N TRP U 14 " --> pdb=" O LEU T 656 " (cutoff:3.500A) removed outlier: 9.474A pdb=" N LEU T 656 " --> pdb=" O TRP U 14 " (cutoff:3.500A) removed outlier: 9.635A pdb=" N TRP U 16 " --> pdb=" O LEU T 654 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N LEU T 654 " --> pdb=" O TRP U 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'T' and resid 700 through 701 Processing sheet with id=AA3, first strand: chain 'U' and resid 64 through 66 Processing sheet with id=AA4, first strand: chain 'C' and resid 29 through 30 Processing sheet with id=AA5, first strand: chain 'C' and resid 74 through 75 removed outlier: 3.931A pdb=" N LYS C 74 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 114 through 120 removed outlier: 3.510A pdb=" N VAL C 124 " --> pdb=" O LEU C 155 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU C 155 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N TYR C 152 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE C 165 " --> pdb=" O TYR C 152 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU C 164 " --> pdb=" O LYS C 368 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ILE C 370 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU C 374 " --> pdb=" O THR C 168 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER C 376 " --> pdb=" O PHE C 215 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE C 215 " --> pdb=" O SER C 376 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C 378 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL C 212 " --> pdb=" O ASP C 207 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP C 207 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N VAL C 204 " --> pdb=" O VAL C 192 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 114 through 120 removed outlier: 3.510A pdb=" N VAL C 124 " --> pdb=" O LEU C 155 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU C 155 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N TYR C 152 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE C 165 " --> pdb=" O TYR C 152 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU C 164 " --> pdb=" O LYS C 368 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ILE C 370 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU C 374 " --> pdb=" O THR C 168 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL C 371 " --> pdb=" O ARG C 219 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG C 219 " --> pdb=" O VAL C 371 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 398 through 405 removed outlier: 3.763A pdb=" N ARG C 450 " --> pdb=" O LEU C 425 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 462 through 467 removed outlier: 6.621A pdb=" N ILE C 462 " --> pdb=" O GLY C 481 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLY C 481 " --> pdb=" O ILE C 462 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA C 464 " --> pdb=" O SER C 479 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR C 492 " --> pdb=" O ILE C 476 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN C 482 " --> pdb=" O GLU C 486 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLU C 486 " --> pdb=" O GLN C 482 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N TYR C 487 " --> pdb=" O ASN C 504 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ASN C 504 " --> pdb=" O TYR C 487 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA C 489 " --> pdb=" O SER C 502 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N SER C 502 " --> pdb=" O ALA C 489 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 925 through 926 removed outlier: 5.728A pdb=" N THR C 925 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE C 994 " --> pdb=" O SER C 986 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 1155 through 1157 Processing sheet with id=AB3, first strand: chain 'C' and resid 1512 through 1513 Processing sheet with id=AB4, first strand: chain 'C' and resid 1564 through 1565 removed outlier: 4.135A pdb=" N ILE C1556 " --> pdb=" O VAL C1565 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL C1555 " --> pdb=" O ILE C1632 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ILE C1634 " --> pdb=" O VAL C1555 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LYS C1557 " --> pdb=" O ILE C1634 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 1584 through 1587 removed outlier: 3.503A pdb=" N ARG C1603 " --> pdb=" O GLU C1571 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER C1601 " --> pdb=" O VAL C1573 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 7 through 9 removed outlier: 6.396A pdb=" N GLY O 8 " --> pdb=" O ILE O 242 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'O' and resid 123 through 124 Processing sheet with id=AB8, first strand: chain 'I' and resid 104 through 105 removed outlier: 4.139A pdb=" N GLU I 104 " --> pdb=" O THR I 112 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR I 112 " --> pdb=" O GLU I 104 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 89 through 90 Processing sheet with id=AC1, first strand: chain 'Q' and resid 11 through 12 removed outlier: 3.616A pdb=" N ASP Q 11 " --> pdb=" O ALA Q 20 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE Q 19 " --> pdb=" O TYR Q 30 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR Q 30 " --> pdb=" O PHE Q 19 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA Q 39 " --> pdb=" O ILE Q 29 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ARG Q 31 " --> pdb=" O ARG Q 37 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ARG Q 37 " --> pdb=" O ARG Q 31 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Q' and resid 49 through 54 removed outlier: 3.902A pdb=" N ASN Q 51 " --> pdb=" O PHE Q 65 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR Q 70 " --> pdb=" O PHE Q 66 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE Q 73 " --> pdb=" O SER Q 84 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER Q 84 " --> pdb=" O ILE Q 73 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ASP Q 75 " --> pdb=" O LEU Q 82 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N LEU Q 82 " --> pdb=" O ASP Q 75 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'Q' and resid 93 through 102 removed outlier: 3.951A pdb=" N LYS Q 95 " --> pdb=" O PHE Q 165 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE Q 165 " --> pdb=" O LYS Q 95 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS Q 171 " --> pdb=" O ASN Q 166 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE Q 172 " --> pdb=" O LEU Q 184 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Q' and resid 124 through 128 Processing sheet with id=AC5, first strand: chain 'Q' and resid 195 through 202 removed outlier: 6.905A pdb=" N PHE Q 209 " --> pdb=" O LYS Q 196 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ILE Q 198 " --> pdb=" O GLN Q 207 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLN Q 207 " --> pdb=" O ILE Q 198 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LYS Q 200 " --> pdb=" O PHE Q 205 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N PHE Q 205 " --> pdb=" O LYS Q 200 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASN Q 219 " --> pdb=" O LEU Q 481 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU Q 481 " --> pdb=" O ASN Q 219 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Q' and resid 496 through 505 removed outlier: 6.900A pdb=" N LEU Q 515 " --> pdb=" O LEU Q 501 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ALA Q 503 " --> pdb=" O VAL Q 513 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL Q 513 " --> pdb=" O ALA Q 503 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LYS Q 505 " --> pdb=" O TYR Q 511 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N TYR Q 511 " --> pdb=" O LYS Q 505 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE Q 538 " --> pdb=" O SER Q 553 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N SER Q 553 " --> pdb=" O ILE Q 538 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Q' and resid 570 through 571 removed outlier: 3.620A pdb=" N ARG Q 570 " --> pdb=" O VAL Q 644 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL Q 644 " --> pdb=" O ARG Q 570 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'Q' and resid 590 through 591 removed outlier: 4.378A pdb=" N ILE Q 618 " --> pdb=" O PHE Q 627 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE Q 627 " --> pdb=" O ILE Q 618 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 31 through 33 removed outlier: 7.215A pdb=" N LEU A 32 " --> pdb=" O GLU A 171 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL A 155 " --> pdb=" O TYR A 167 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N MET A 169 " --> pdb=" O VAL A 153 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL A 153 " --> pdb=" O MET A 169 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ARG A 199 " --> pdb=" O TYR A 156 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N CYS A 195 " --> pdb=" O MET A 131 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N MET A 131 " --> pdb=" O CYS A 195 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N PHE A 197 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 11.491A pdb=" N LYS A 129 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 11.287A pdb=" N ARG A 199 " --> pdb=" O PHE A 127 " (cutoff:3.500A) removed outlier: 11.597A pdb=" N PHE A 127 " --> pdb=" O ARG A 199 " (cutoff:3.500A) removed outlier: 11.192A pdb=" N LEU A 201 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 11.866A pdb=" N ILE A 125 " --> pdb=" O LEU A 201 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 82 through 83 removed outlier: 4.133A pdb=" N GLY A 216 " --> pdb=" O PHE A 139 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 135 " --> pdb=" O TYR A 220 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 113 through 114 removed outlier: 3.641A pdb=" N TRP A 113 " --> pdb=" O LEU A 214 " (cutoff:3.500A) 3336 hydrogen bonds defined for protein. 9843 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 22.77 Time building geometry restraints manager: 20.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 18083 1.34 - 1.47: 14719 1.47 - 1.60: 25822 1.60 - 1.74: 0 1.74 - 1.87: 455 Bond restraints: 59079 Sorted by residual: bond pdb=" CG GLU F 564 " pdb=" CD GLU F 564 " ideal model delta sigma weight residual 1.516 1.448 0.068 2.50e-02 1.60e+03 7.34e+00 bond pdb=" C ASP J 667 " pdb=" O ASP J 667 " ideal model delta sigma weight residual 1.235 1.222 0.013 4.70e-03 4.53e+04 7.09e+00 bond pdb=" CG ARG F 635 " pdb=" CD ARG F 635 " ideal model delta sigma weight residual 1.520 1.448 0.072 3.00e-02 1.11e+03 5.79e+00 bond pdb=" CG GLU H 179 " pdb=" CD GLU H 179 " ideal model delta sigma weight residual 1.516 1.456 0.060 2.50e-02 1.60e+03 5.75e+00 bond pdb=" CG LEU Q 376 " pdb=" CD1 LEU Q 376 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.72e+00 ... (remaining 59074 not shown) Histogram of bond angle deviations from ideal: 92.04 - 100.47: 54 100.47 - 108.90: 3019 108.90 - 117.33: 38620 117.33 - 125.77: 37480 125.77 - 134.20: 793 Bond angle restraints: 79966 Sorted by residual: angle pdb=" N GLU F 564 " pdb=" CA GLU F 564 " pdb=" CB GLU F 564 " ideal model delta sigma weight residual 110.12 120.92 -10.80 1.47e+00 4.63e-01 5.40e+01 angle pdb=" N PRO C 845 " pdb=" CA PRO C 845 " pdb=" CB PRO C 845 " ideal model delta sigma weight residual 103.25 110.21 -6.96 1.05e+00 9.07e-01 4.40e+01 angle pdb=" CA GLU J 484 " pdb=" CB GLU J 484 " pdb=" CG GLU J 484 " ideal model delta sigma weight residual 114.10 126.82 -12.72 2.00e+00 2.50e-01 4.04e+01 angle pdb=" N GLU J 484 " pdb=" CA GLU J 484 " pdb=" CB GLU J 484 " ideal model delta sigma weight residual 110.01 119.11 -9.10 1.45e+00 4.76e-01 3.94e+01 angle pdb=" CA GLU F 564 " pdb=" CB GLU F 564 " pdb=" CG GLU F 564 " ideal model delta sigma weight residual 114.10 124.95 -10.85 2.00e+00 2.50e-01 2.94e+01 ... (remaining 79961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 32278 18.00 - 35.99: 2772 35.99 - 53.99: 372 53.99 - 71.99: 52 71.99 - 89.98: 39 Dihedral angle restraints: 35513 sinusoidal: 14095 harmonic: 21418 Sorted by residual: dihedral pdb=" CA THR T 620 " pdb=" C THR T 620 " pdb=" N GLN T 621 " pdb=" CA GLN T 621 " ideal model delta harmonic sigma weight residual 180.00 130.38 49.62 0 5.00e+00 4.00e-02 9.85e+01 dihedral pdb=" CA SER T 623 " pdb=" C SER T 623 " pdb=" N ASN T 624 " pdb=" CA ASN T 624 " ideal model delta harmonic sigma weight residual 180.00 133.21 46.79 0 5.00e+00 4.00e-02 8.76e+01 dihedral pdb=" CA GLY T 622 " pdb=" C GLY T 622 " pdb=" N SER T 623 " pdb=" CA SER T 623 " ideal model delta harmonic sigma weight residual 180.00 134.39 45.61 0 5.00e+00 4.00e-02 8.32e+01 ... (remaining 35510 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 8159 0.083 - 0.167: 784 0.167 - 0.250: 75 0.250 - 0.334: 11 0.334 - 0.417: 2 Chirality restraints: 9031 Sorted by residual: chirality pdb=" CG LEU F 181 " pdb=" CB LEU F 181 " pdb=" CD1 LEU F 181 " pdb=" CD2 LEU F 181 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.35e+00 chirality pdb=" CA GLU K 284 " pdb=" N GLU K 284 " pdb=" C GLU K 284 " pdb=" CB GLU K 284 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" CA GLU J 484 " pdb=" N GLU J 484 " pdb=" C GLU J 484 " pdb=" CB GLU J 484 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.74e+00 ... (remaining 9028 not shown) Planarity restraints: 10103 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS U 74 " 0.031 2.00e-02 2.50e+03 3.64e-02 1.99e+01 pdb=" CG HIS U 74 " -0.078 2.00e-02 2.50e+03 pdb=" ND1 HIS U 74 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 HIS U 74 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 HIS U 74 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS U 74 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE T 518 " 0.030 2.00e-02 2.50e+03 3.16e-02 1.75e+01 pdb=" CG PHE T 518 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 PHE T 518 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE T 518 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 PHE T 518 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE T 518 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE T 518 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 503 " 0.041 2.00e-02 2.50e+03 2.82e-02 1.59e+01 pdb=" CG TYR J 503 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TYR J 503 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR J 503 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR J 503 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR J 503 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR J 503 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR J 503 " 0.003 2.00e-02 2.50e+03 ... (remaining 10100 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 579 2.58 - 3.16: 51358 3.16 - 3.74: 94573 3.74 - 4.32: 122574 4.32 - 4.90: 197509 Nonbonded interactions: 466593 Sorted by model distance: nonbonded pdb=" CD2 HIS U 71 " pdb="ZN ZN U 202 " model vdw 1.998 1.960 nonbonded pdb=" O SER T 623 " pdb=" N ASP T 625 " model vdw 2.041 2.520 nonbonded pdb=" O LEU K 569 " pdb=" ND1 HIS K 573 " model vdw 2.071 2.520 nonbonded pdb=" O VAL O 216 " pdb=" NE2 GLN O 220 " model vdw 2.072 2.520 nonbonded pdb=" OG SER O 291 " pdb=" OD1 ASN O 293 " model vdw 2.098 2.440 ... (remaining 466588 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'D' and (resid 6 through 44 or resid 75 through 143 or (resid 144 and (na \ me N or name CA or name C or name O or name CB )) or resid 145 or (resid 146 and \ (name N or name CA or name C or name O or name CB )) or resid 184 through 198 o \ r (resid 199 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 00 through 201 or (resid 202 and (name N or name CA or name C or name O or name \ CB )) or resid 203 through 340 or (resid 341 and (name N or name CA or name C or \ name O or name CB )) or resid 342 through 343 or (resid 344 and (name N or name \ CA or name C or name O or name CB )) or resid 345 through 349 or (resid 350 and \ (name N or name CA or name C or name O or name CB )) or resid 351 through 439 o \ r (resid 440 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 41 through 555 or (resid 556 and (name N or name CA or name C or name O or name \ CB )) or resid 557 through 575 or (resid 576 and (name N or name CA or name C or \ name O or name CB )) or resid 577 through 626)) selection = (chain 'P' and (resid 6 through 86 or (resid 87 and (name N or name CA or name C \ or name O or name CB )) or resid 88 through 146 or resid 184 through 278 or (re \ sid 279 and (name N or name CA or name C or name O or name CB )) or resid 280 th \ rough 510 or (resid 511 and (name N or name CA or name C or name O or name CB )) \ or resid 512 through 610 or (resid 611 and (name N or name CA or name C or name \ O or name CB )) or resid 612 through 613 or (resid 614 through 616 and (name N \ or name CA or name C or name O or name CB )) or resid 617 through 619 or (resid \ 620 through 621 and (name N or name CA or name C or name O or name CB )) or resi \ d 622 or (resid 623 through 626 and (name N or name CA or name C or name O or na \ me CB )))) } ncs_group { reference = (chain 'F' and (resid 23 through 130 or (resid 131 and (name N or name CA or nam \ e C or name O or name CB )) or resid 143 through 208 or (resid 209 and (name N o \ r name CA or name C or name O or name CB )) or resid 432 through 445 or (resid 4 \ 46 and (name N or name CA or name C or name O or name CB )) or resid 447 through \ 755)) selection = (chain 'H' and (resid 23 through 55 or (resid 56 and (name N or name CA or name \ C or name O or name CB )) or resid 57 through 60 or (resid 61 through 62 and (na \ me N or name CA or name C or name O or name CB )) or resid 63 through 111 or (re \ sid 112 through 113 and (name N or name CA or name C or name O or name CB )) or \ resid 114 through 131 or resid 143 through 197 or (resid 198 through 199 and (na \ me N or name CA or name C or name O or name CB )) or resid 200 through 453 or (r \ esid 454 through 455 and (name N or name CA or name C or name O or name CB )) or \ resid 456 through 459 or (resid 460 and (name N or name CA or name C or name O \ or name CB )) or resid 461 through 569 or (resid 570 and (name N or name CA or n \ ame C or name O or name CB )) or resid 571 through 755)) } ncs_group { reference = chain 'G' selection = chain 'W' } ncs_group { reference = (chain 'J' and (resid 229 through 326 or resid 352 through 508 or (resid 509 and \ (name N or name CA or name C or name O or name CB )) or resid 510 through 748 o \ r (resid 749 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 50 through 757 or (resid 758 and (name N or name CA or name C or name O or name \ CB )))) selection = (chain 'K' and (resid 229 through 231 or (resid 232 and (name N or name CA or na \ me C or name O or name CB )) or resid 233 through 254 or (resid 255 and (name N \ or name CA or name C or name O or name CB )) or resid 256 through 326 or (resid \ 352 and (name N or name CA or name C or name O or name CB )) or resid 353 throug \ h 388 or (resid 389 and (name N or name CA or name C or name O or name CB )) or \ resid 390 through 758)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 6.010 Check model and map are aligned: 0.690 Set scattering table: 0.420 Process input model: 129.130 Find NCS groups from input model: 2.440 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 142.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 59079 Z= 0.266 Angle : 0.881 15.224 79966 Z= 0.451 Chirality : 0.051 0.417 9031 Planarity : 0.005 0.093 10103 Dihedral : 13.250 89.982 21597 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 18.51 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.89 % Favored : 95.76 % Rotamer: Outliers : 0.05 % Allowed : 1.12 % Favored : 98.83 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.10), residues: 7101 helix: 1.48 (0.08), residues: 4431 sheet: 0.44 (0.29), residues: 325 loop : -1.19 (0.13), residues: 2345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP D 35 HIS 0.043 0.002 HIS U 74 PHE 0.073 0.002 PHE T 518 TYR 0.067 0.002 TYR J 503 ARG 0.054 0.001 ARG D 14 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14202 Ramachandran restraints generated. 7101 Oldfield, 0 Emsley, 7101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14202 Ramachandran restraints generated. 7101 Oldfield, 0 Emsley, 7101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 989 residues out of total 6549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 986 time to evaluate : 5.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 989 average time/residue: 0.5832 time to fit residues: 989.0911 Evaluate side-chains 670 residues out of total 6549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 670 time to evaluate : 5.321 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.9923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 714 random chunks: chunk 602 optimal weight: 8.9990 chunk 541 optimal weight: 10.0000 chunk 300 optimal weight: 7.9990 chunk 184 optimal weight: 6.9990 chunk 365 optimal weight: 3.9990 chunk 289 optimal weight: 40.0000 chunk 559 optimal weight: 8.9990 chunk 216 optimal weight: 9.9990 chunk 340 optimal weight: 0.9980 chunk 416 optimal weight: 0.8980 chunk 648 optimal weight: 0.9980 overall best weight: 2.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 31 GLN ** F 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 697 GLN ** J 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 521 HIS ** J 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 750 ASN J 755 ASN ** K 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 732 HIS W 13 HIS H 638 ASN ** U 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 611 GLN C 648 HIS ** C 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 789 ASN ** C 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1056 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1137 ASN ** C1140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1265 ASN C1510 GLN ** C1514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 248 GLN ** O 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 339 HIS D 371 ASN D 377 GLN D 391 GLN ** D 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 535 ASN ** P 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 327 ASN ** P 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 15 HIS ** I 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 64 ASN A 121 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 59079 Z= 0.237 Angle : 0.667 10.560 79966 Z= 0.349 Chirality : 0.042 0.302 9031 Planarity : 0.004 0.056 10103 Dihedral : 4.486 52.586 7776 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.03 % Favored : 95.73 % Rotamer: Outliers : 0.24 % Allowed : 5.68 % Favored : 94.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.10), residues: 7101 helix: 1.24 (0.07), residues: 4609 sheet: 0.50 (0.28), residues: 331 loop : -1.11 (0.14), residues: 2161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP D 35 HIS 0.018 0.001 HIS U 71 PHE 0.042 0.002 PHE F 495 TYR 0.035 0.002 TYR J 503 ARG 0.013 0.001 ARG T 510 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14202 Ramachandran restraints generated. 7101 Oldfield, 0 Emsley, 7101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14202 Ramachandran restraints generated. 7101 Oldfield, 0 Emsley, 7101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 925 residues out of total 6549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 910 time to evaluate : 5.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 5 residues processed: 921 average time/residue: 0.5335 time to fit residues: 843.5864 Evaluate side-chains 600 residues out of total 6549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 595 time to evaluate : 5.312 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.5818 time to fit residues: 11.7370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 714 random chunks: chunk 360 optimal weight: 7.9990 chunk 201 optimal weight: 8.9990 chunk 539 optimal weight: 5.9990 chunk 441 optimal weight: 6.9990 chunk 178 optimal weight: 5.9990 chunk 649 optimal weight: 0.0980 chunk 701 optimal weight: 9.9990 chunk 578 optimal weight: 0.9990 chunk 644 optimal weight: 7.9990 chunk 221 optimal weight: 4.9990 chunk 521 optimal weight: 6.9990 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 31 GLN ** F 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 697 GLN ** J 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 750 ASN K 374 ASN K 551 GLN ** K 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 732 HIS ** T 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 595 HIS U 6 ASN C 463 GLN ** C 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 789 ASN C 901 ASN ** C 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 248 GLN O 387 ASN D 341 ASN ** D 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 535 ASN P 11 HIS ** P 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 379 ASN ** P 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 521 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 59079 Z= 0.252 Angle : 0.642 11.047 79966 Z= 0.335 Chirality : 0.041 0.255 9031 Planarity : 0.004 0.115 10103 Dihedral : 4.509 50.003 7776 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.10 % Favored : 95.66 % Rotamer: Outliers : 0.14 % Allowed : 4.53 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.10), residues: 7101 helix: 1.18 (0.07), residues: 4614 sheet: 0.36 (0.27), residues: 332 loop : -1.11 (0.14), residues: 2155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 35 HIS 0.035 0.001 HIS U 74 PHE 0.030 0.002 PHE O 326 TYR 0.027 0.002 TYR F 176 ARG 0.008 0.001 ARG T 510 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14202 Ramachandran restraints generated. 7101 Oldfield, 0 Emsley, 7101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14202 Ramachandran restraints generated. 7101 Oldfield, 0 Emsley, 7101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 6549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 860 time to evaluate : 5.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 868 average time/residue: 0.5469 time to fit residues: 818.9277 Evaluate side-chains 597 residues out of total 6549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 594 time to evaluate : 5.379 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4856 time to fit residues: 10.8262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 714 random chunks: chunk 641 optimal weight: 0.1980 chunk 488 optimal weight: 4.9990 chunk 337 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 309 optimal weight: 0.6980 chunk 436 optimal weight: 1.9990 chunk 651 optimal weight: 9.9990 chunk 690 optimal weight: 30.0000 chunk 340 optimal weight: 1.9990 chunk 617 optimal weight: 9.9990 chunk 185 optimal weight: 30.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 31 GLN F 548 ASN ** F 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 609 ASN F 697 GLN ** J 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 690 ASN J 750 ASN ** K 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 732 HIS H 184 ASN ** E 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 789 ASN ** C1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1214 ASN C1265 ASN ** C1372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 308 ASN D 341 ASN ** D 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 479 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 59079 Z= 0.190 Angle : 0.601 10.518 79966 Z= 0.311 Chirality : 0.041 0.240 9031 Planarity : 0.004 0.080 10103 Dihedral : 4.443 48.938 7776 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.08 % Favored : 95.69 % Rotamer: Outliers : 0.13 % Allowed : 3.41 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.10), residues: 7101 helix: 1.20 (0.08), residues: 4626 sheet: 0.37 (0.27), residues: 324 loop : -1.09 (0.14), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP P 128 HIS 0.041 0.001 HIS U 74 PHE 0.036 0.002 PHE D 299 TYR 0.023 0.001 TYR H 191 ARG 0.010 0.000 ARG T 510 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14202 Ramachandran restraints generated. 7101 Oldfield, 0 Emsley, 7101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14202 Ramachandran restraints generated. 7101 Oldfield, 0 Emsley, 7101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 870 residues out of total 6549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 862 time to evaluate : 5.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 867 average time/residue: 0.5498 time to fit residues: 820.5441 Evaluate side-chains 602 residues out of total 6549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 600 time to evaluate : 5.385 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4981 time to fit residues: 9.0092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 714 random chunks: chunk 574 optimal weight: 0.9980 chunk 391 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 513 optimal weight: 1.9990 chunk 284 optimal weight: 50.0000 chunk 588 optimal weight: 20.0000 chunk 477 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 352 optimal weight: 0.5980 chunk 619 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 31 GLN ** F 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 697 GLN ** J 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 750 ASN ** K 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 732 HIS K 741 ASN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 462 HIS ** U 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 789 ASN ** C1140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 172 ASN ** O 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 308 ASN D 341 ASN D 489 GLN ** D 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 406 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 59079 Z= 0.194 Angle : 0.598 11.057 79966 Z= 0.308 Chirality : 0.041 0.262 9031 Planarity : 0.004 0.078 10103 Dihedral : 4.403 47.675 7776 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.14 % Favored : 95.63 % Rotamer: Outliers : 0.05 % Allowed : 3.42 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.10), residues: 7101 helix: 1.27 (0.08), residues: 4624 sheet: 0.28 (0.27), residues: 325 loop : -1.10 (0.14), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP P 128 HIS 0.034 0.001 HIS U 71 PHE 0.049 0.002 PHE J 571 TYR 0.021 0.001 TYR A 167 ARG 0.011 0.000 ARG N 139 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14202 Ramachandran restraints generated. 7101 Oldfield, 0 Emsley, 7101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14202 Ramachandran restraints generated. 7101 Oldfield, 0 Emsley, 7101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 857 residues out of total 6549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 854 time to evaluate : 5.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 857 average time/residue: 0.5518 time to fit residues: 817.9031 Evaluate side-chains 610 residues out of total 6549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 608 time to evaluate : 5.840 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4995 time to fit residues: 8.8561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 714 random chunks: chunk 232 optimal weight: 0.7980 chunk 621 optimal weight: 7.9990 chunk 136 optimal weight: 8.9990 chunk 405 optimal weight: 40.0000 chunk 170 optimal weight: 9.9990 chunk 690 optimal weight: 30.0000 chunk 573 optimal weight: 8.9990 chunk 319 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 228 optimal weight: 6.9990 chunk 362 optimal weight: 20.0000 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 31 GLN F 81 ASN F 439 ASN ** F 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 732 HIS J 750 ASN ** K 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 637 ASN K 732 HIS H 117 ASN ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 689 GLN U 9 HIS ** U 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 789 ASN ** C 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1510 GLN ** C1514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN D 371 ASN ** D 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 HIS ** P 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 364 ASN ** P 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 406 HIS ** Q 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.143 59079 Z= 0.298 Angle : 0.678 11.238 79966 Z= 0.358 Chirality : 0.042 0.248 9031 Planarity : 0.004 0.067 10103 Dihedral : 4.671 45.447 7776 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.91 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.10), residues: 7101 helix: 0.96 (0.07), residues: 4626 sheet: 0.10 (0.27), residues: 326 loop : -1.17 (0.14), residues: 2149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP P 128 HIS 0.049 0.002 HIS U 74 PHE 0.036 0.002 PHE T 518 TYR 0.026 0.002 TYR H 191 ARG 0.009 0.001 ARG E 175 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14202 Ramachandran restraints generated. 7101 Oldfield, 0 Emsley, 7101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14202 Ramachandran restraints generated. 7101 Oldfield, 0 Emsley, 7101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 6549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 776 time to evaluate : 5.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 776 average time/residue: 0.5524 time to fit residues: 745.9555 Evaluate side-chains 550 residues out of total 6549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 550 time to evaluate : 5.332 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.0929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 714 random chunks: chunk 666 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 393 optimal weight: 0.6980 chunk 504 optimal weight: 10.0000 chunk 390 optimal weight: 0.9990 chunk 581 optimal weight: 3.9990 chunk 385 optimal weight: 5.9990 chunk 688 optimal weight: 10.0000 chunk 430 optimal weight: 1.9990 chunk 419 optimal weight: 30.0000 chunk 317 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 31 GLN ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 551 GLN ** J 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 750 ASN ** K 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 732 HIS ** E 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 689 GLN ** U 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 789 ASN ** C1140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 308 ASN D 341 ASN D 371 ASN ** D 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 371 ASN ** P 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 307 ASN ** Q 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 406 HIS ** Q 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 59079 Z= 0.178 Angle : 0.620 11.743 79966 Z= 0.314 Chirality : 0.041 0.231 9031 Planarity : 0.004 0.063 10103 Dihedral : 4.495 44.342 7776 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.03 % Favored : 95.73 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.10), residues: 7101 helix: 1.16 (0.08), residues: 4629 sheet: 0.03 (0.27), residues: 341 loop : -1.14 (0.14), residues: 2131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP P 249 HIS 0.028 0.001 HIS U 74 PHE 0.033 0.002 PHE D 299 TYR 0.036 0.001 TYR O 482 ARG 0.010 0.000 ARG F 691 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14202 Ramachandran restraints generated. 7101 Oldfield, 0 Emsley, 7101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14202 Ramachandran restraints generated. 7101 Oldfield, 0 Emsley, 7101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 6549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 845 time to evaluate : 5.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 845 average time/residue: 0.5621 time to fit residues: 824.4951 Evaluate side-chains 594 residues out of total 6549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 594 time to evaluate : 5.346 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.0179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 714 random chunks: chunk 425 optimal weight: 2.9990 chunk 274 optimal weight: 9.9990 chunk 411 optimal weight: 4.9990 chunk 207 optimal weight: 9.9990 chunk 135 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 chunk 437 optimal weight: 4.9990 chunk 468 optimal weight: 0.7980 chunk 340 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 chunk 540 optimal weight: 8.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 31 GLN ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 750 ASN ** K 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 732 HIS ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 587 ASN ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 462 HIS ** U 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 789 ASN ** C1140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1510 GLN ** C1514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 308 ASN D 341 ASN D 371 ASN ** D 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 307 ASN ** Q 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 406 HIS ** Q 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 86 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 59079 Z= 0.228 Angle : 0.644 12.716 79966 Z= 0.334 Chirality : 0.042 0.301 9031 Planarity : 0.004 0.086 10103 Dihedral : 4.574 43.271 7776 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.60 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.10), residues: 7101 helix: 1.07 (0.08), residues: 4621 sheet: -0.01 (0.27), residues: 331 loop : -1.15 (0.14), residues: 2149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP P 128 HIS 0.061 0.001 HIS U 74 PHE 0.056 0.002 PHE J 267 TYR 0.031 0.002 TYR J 279 ARG 0.010 0.000 ARG F 691 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14202 Ramachandran restraints generated. 7101 Oldfield, 0 Emsley, 7101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14202 Ramachandran restraints generated. 7101 Oldfield, 0 Emsley, 7101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 6549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 779 time to evaluate : 5.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 779 average time/residue: 0.5494 time to fit residues: 746.0254 Evaluate side-chains 551 residues out of total 6549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 551 time to evaluate : 5.339 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.0500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 714 random chunks: chunk 626 optimal weight: 2.9990 chunk 659 optimal weight: 8.9990 chunk 601 optimal weight: 3.9990 chunk 641 optimal weight: 5.9990 chunk 385 optimal weight: 3.9990 chunk 279 optimal weight: 0.0670 chunk 503 optimal weight: 0.9980 chunk 196 optimal weight: 0.8980 chunk 579 optimal weight: 4.9990 chunk 606 optimal weight: 5.9990 chunk 639 optimal weight: 0.5980 overall best weight: 1.1120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 31 GLN F 81 ASN ** F 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 750 ASN ** K 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 551 GLN ** K 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 732 HIS ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 HIS ** C 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 789 ASN ** C1140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 246 HIS D 341 ASN D 371 ASN ** D 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 371 ASN ** P 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 307 ASN ** Q 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 406 HIS ** Q 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 59079 Z= 0.181 Angle : 0.643 12.369 79966 Z= 0.326 Chirality : 0.042 0.259 9031 Planarity : 0.004 0.078 10103 Dihedral : 4.518 42.931 7776 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.31 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.10), residues: 7101 helix: 1.15 (0.08), residues: 4617 sheet: 0.09 (0.28), residues: 331 loop : -1.18 (0.14), residues: 2153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP N 116 HIS 0.043 0.001 HIS U 74 PHE 0.049 0.002 PHE F 495 TYR 0.028 0.001 TYR N 104 ARG 0.010 0.000 ARG F 691 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14202 Ramachandran restraints generated. 7101 Oldfield, 0 Emsley, 7101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14202 Ramachandran restraints generated. 7101 Oldfield, 0 Emsley, 7101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 802 residues out of total 6549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 802 time to evaluate : 5.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 802 average time/residue: 0.5651 time to fit residues: 791.6278 Evaluate side-chains 584 residues out of total 6549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 584 time to evaluate : 5.405 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.1641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 714 random chunks: chunk 421 optimal weight: 4.9990 chunk 678 optimal weight: 20.0000 chunk 413 optimal weight: 0.9990 chunk 321 optimal weight: 0.9980 chunk 471 optimal weight: 2.9990 chunk 711 optimal weight: 9.9990 chunk 654 optimal weight: 0.9980 chunk 566 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 437 optimal weight: 1.9990 chunk 347 optimal weight: 0.4980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 31 GLN ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 750 ASN ** K 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 732 HIS ** E 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 789 ASN ** C 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1510 GLN ** C1514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 ASN ** D 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 371 ASN ** P 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 406 HIS ** Q 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 650 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 59079 Z= 0.178 Angle : 0.651 15.924 79966 Z= 0.328 Chirality : 0.042 0.281 9031 Planarity : 0.004 0.071 10103 Dihedral : 4.500 42.108 7776 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.39 % Favored : 95.38 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.10), residues: 7101 helix: 1.13 (0.08), residues: 4608 sheet: 0.13 (0.28), residues: 329 loop : -1.19 (0.14), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP P 128 HIS 0.040 0.001 HIS U 74 PHE 0.037 0.002 PHE J 267 TYR 0.035 0.001 TYR E 236 ARG 0.009 0.000 ARG F 691 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14202 Ramachandran restraints generated. 7101 Oldfield, 0 Emsley, 7101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14202 Ramachandran restraints generated. 7101 Oldfield, 0 Emsley, 7101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 6549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 811 time to evaluate : 5.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 811 average time/residue: 0.5362 time to fit residues: 759.3300 Evaluate side-chains 588 residues out of total 6549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 588 time to evaluate : 7.457 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.4917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 714 random chunks: chunk 449 optimal weight: 5.9990 chunk 603 optimal weight: 10.0000 chunk 173 optimal weight: 7.9990 chunk 522 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 157 optimal weight: 6.9990 chunk 567 optimal weight: 0.8980 chunk 237 optimal weight: 8.9990 chunk 582 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 31 GLN ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 487 ASN ** F 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 609 ASN ** F 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 750 ASN ** K 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 732 HIS ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 789 ASN ** C 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1140 HIS ** C1184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1265 ASN C1280 ASN ** C1372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 226 ASN ** O 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN ** D 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 405 ASN ** D 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 ASN ** Q 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 406 HIS ** Q 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 650 GLN ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.089321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.060584 restraints weight = 326871.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.062471 restraints weight = 196796.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.063771 restraints weight = 135137.430| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 59079 Z= 0.242 Angle : 0.670 12.054 79966 Z= 0.347 Chirality : 0.042 0.251 9031 Planarity : 0.004 0.069 10103 Dihedral : 4.602 39.846 7776 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.73 % Favored : 95.04 % Rotamer: Outliers : 0.02 % Allowed : 0.44 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.10), residues: 7101 helix: 1.05 (0.08), residues: 4618 sheet: -0.04 (0.27), residues: 340 loop : -1.20 (0.14), residues: 2143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP P 128 HIS 0.036 0.001 HIS U 74 PHE 0.044 0.002 PHE T 112 TYR 0.031 0.002 TYR E 236 ARG 0.009 0.001 ARG D 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13065.70 seconds wall clock time: 231 minutes 43.30 seconds (13903.30 seconds total)